A Different Beginning
by Super Eri
Summary: A different take on the Connor/Clark dynamic and how it might change if there was another young Kent. The summary is a little lame, but give the story a chance. Thanks.
1. Chapter 1

Author's note: This is my little AU idea. I love Young Justice and I am a huge Superman fan, but I hate how cold he is in the series. I think it is ooc for him and I'd like to see that relationship change. This story is just a take on how that could happen if Clark Kent already had a daughter and she joined Young Justice.

Chapter One

Her purple painted fingernails sped across the keyboard as she worked to finish her report. She heard the familiar "whoosh" of her father entering the house through the open bedroom door. She stopped and waved a little smoke from her keyboard, she guessed she was going a little too fast. She had gotten the message earlier that her father was still unreceptive to the "situation." She had been waiting patiently and now it was her turn to put her plan into action.

Clark made his way down the stairs after changing out of his suit. He had done a couple rescuers after that "talk "with Bruce. He had needed to get his mind off of it.

"Dad." Clark heard the voice of his daughter. There was something in her voice that he hadn't heard before. Her voice was laced with something; it wasn't anger, but something close. She saw his thirteen year old daughter at the bottom of the steps with her arms folded in front of her. He got to the bottom of the steps and looked into her blue eye, and then he knew, it was disappointment.

"Why didn't you tell me I had a brother?"

"How…" He trailed off, he knew how she knew, damn Dick Grayson. Between Bruce and his ward he wasn't going to able to ignore this "situation."

"Where is your mother?" He asked. He silently, hoped she hadn't told Lois.

"She's working, don't worry I didn't tell her… yet."

"Listen Caelyn, I don't know what Dick told you, but…."

" But what? You didn't want me or mom or grandma and grandpa to know that his boy existed and you have no intention of dealing with him? What were you going to do, just dump him on the Justice League and think no one was going to find out?" She raised her eyebrow. He sighed, she was so straight forward, so much like her mother, maybe too much for his sake.

"Please just let me say something," he said and looked at her to see if she would let him continue. He led her to the couch and sat them both down.

"This is all just so disconcerting. Do you understand how he got here? He was created from my DNA. They stole it somehow. He was created as a weapon, probably to use against me. I just don't know how I'm supposed to react." He said, finally letting himself vent.

"Well is ignoring him the right thing to do?" She asked honestly, there wasn't any sarcasm in her words.

"He probably feels scared and alone, but he isn't alone. He doesn't have to feel that way. We can help him can't we? "

"I don't know what he is capable of. Batman says he has a lot of anger."

And Robin says he is a good guy. He just needs help from people like him, he needs us."

"When did you get so insightful?" he asked honestly. She just smiled in response. It seemed like just yesterday she was his little girl, but their conversation was showing how much she was growing up.

"So what are we going to do?" she asked

"I'm being honest here. I don't know how this is going to work out. I'm just trying to adjust to all this. I just need more time."

"Okay," she said slowly. "Then I have an idea." Clark didn't miss how her eyes lit up a bit. He let her continue, not sure where his daughter was headed.

"You let me join the new team and in exchange I will give you another month to adjust before I tell anyone." Clark's mouth fell open slightly, was his daughter blackmailing him?

"Wait. This isn't fair. Caelyn your too young, your powers…." She cut him off

"Dick is the same age and my powers have been developing since I was a baby. Mom told me stories about how I'd float out of my crib. I want to do what you do. I want to be a hero like you someday and this is the perfect way for me to train. I can learn so much." Her eyes were pleading a bit, but she also knew she had the upper hand.

"You are not making this any easier on me Cael, you do realize that don't you?" he said as he let his head go back and hit the pillows of the couch.

Caelyn giggled a bit over her victory, but then got up and hugged her father.

"It is all going to be okay, daddy," she whispered.

Dick got her message. He went to Bruce's' study and opened the door.

He smiled wide and said only, "Plan B for Operation Super Dad is complete. We have a supergirl."

The team (Atriums is not on the team yet) was gathered in the main hall of Mount Justice. They were told they were going to be introduced to someone. Robin was forcing down his smile, as to not give it away.

The zeta tubes announced the arrival of the visitor, Batman 02, Supergirl B 07." Superboy's eyes went wide with the announcement of the second person. He say her appear. She had on a uniform similar to Superman's, but it included a skirt, short sleeves and a shorter cape. She stood next to Batman smiling, then she saw him. Their identical blue eyes met and locked. The boy quickly turned angry, it was an easy emotion for him.

"What is this? Did he do this? Who is she, my replacement?" He yelled. The rest of team seemed shocked, Caelyn stepped forward.

"No, I'm you sister," she stated simply. Superboy's eyes went wide again.

Just a note- If you haven't figured it out, Caelyn know the identities of Robin and Batman, more of that backstory to come.

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	2. Chapter 2

Chapter 2

Batman ushered the rest of the team to do a training simulation. The two super kids stood awkwardly for a minute, Superboy spoke first.

"So you're his daughter?"

"Yes."

"So I guess his isn't opposed to kids in general, just me," he said flatly. Caelyn wanted respond with a resounding no, but instead she took a minute to think.

"It's not you, it is the situation. He will come around and in the meantime I'd like to get to know my brother."

Superboy stared blankly for a moment, not sure what to think. In the short time he's been on this earth he had learned to be angry and skeptical, but there was something about this girl. Something told him that even if Superman never accepted him that he would still have family. He couldn't pass that up.

"Okay," he said with a smile.

"Cool," she said reaching up to her blond hair and removing the wig, she revealed light brown locks. Superboy raised an eyebrow.

"It's part of my secret identity," she said in an excited whisper as she reached into a secret pocket and pulled out a pair of black rimmed glasses and put them on.

"I guess I should introduce myself. My name is Caelyn Lane Kent," she said extending her hand.

"They call me… um Superboy," he said nervously. He felt awkward that he didn't have a name.

Caelyn realized as soon as she said her full name that she may not be approaching this the right way. She thought quickly of how she could recover.

"Connor," she said.

"What?'"

"How about Connor? Connor Kent, it has a certain ring to it doesn't it?

"Connor," he tried it out. "Yeah, okay."

With a smile on his face he extended his hand, "hi, I'm Connor." They shook hands.

Caelyn floated in the air with her hands behind her head as her brother fell to the ground again.

"Connor, try to relax," she coaxed trying to figure a way to help him. She could tell Connor was frustrated. He wanted to learn how to fly, and while Caelyn could fly, she wasn't sure how to translate her abilities. Frankly she was getting frustrated too. It had been nearly a month and still her dad was trying everything to avoid Connor and by extension her. He was working and rescuing way more. She wondered just how long he could keep it up.

"This is hopeless. I can't do it," he said letting his fist sink into the wall and leaving a sizable hole. Wally, who was walking through the hall at the time, poked his head through and smiled.

"So I guess flying lessons are going well." Connor just growled in response and Kid Flash moved on quickly.

"You tried, but I just can't," he said calmer this time.

"You just need more help," she said standing in front of him.

"I need his help." He frowned and she nodded sadly.

"Listen, I have to go, but I will talk to him, and then I will be back to spend the weekend," she said grabbing her backpack.

Caelyn left Connor in the training room and made her way to the zeta tubes. Robin caught her as she passed the kitchen.

"Hey Supergirl."

"Hi Robin." The two thirteen year olds used their hero identities, both forbidden to tell who they really were.

"So how's it going?" he asked. Caelyn rolled her eyes in response.

"He is just so stubborn. I know I did the right thing. Connor needed to know that he had support, but I'm just not sure how this is going to turn out anymore. He barely talks to me. Mom is getting suspicious. I have no idea how she will react. I'm just worried. I got a brother, but at what cost? Does it even out if both my parents are going to hate me. It is just so much pressure."

"Well try to stay whelmed. It takes a lot of guts to blackmail Superman," he said with a chuckle.

She let out a huff. "Thanks for that," she said.

He stopped walking, grabbed her shoulders and turned her to face him. He looked her in the eyes tilting his glasses down slightly to reveal his brilliant blue eyes.

"If it means anything, I think you did the right thing too."

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	3. Chapter 3

Chapter 3

Talking with Dick helped, but she was most certainly overwhelmed. She got home in time for dinner as she saw her mom setting the table and her dad bringing the meal out. She stood just inside the door and took in her surroundings. She looked at her mother; she could see the worry in her eyes. Why had she thought she could keep anything from Lois Lane? She looked to her father and his eyes averted hers. She knew then it was time.

"I'm sorry Dad. This is it. We need to face this. No more hiding," she said. She saw him open his mouth to protest, but then stop. She sighed.

"Mom, I've been lying about what I've been doing after school. I joined a team formed by the Justice League for young superheroes. The reason Dad allowed me to do it and didn't tell you is because I blackmailed him."

Lois Lane looked at her daughter in disbelief. What in the world could her thirteen year old daughter have to blackmail her super hero father with? Lois nearly laughed, she was a world renowned investigative reporter, but she seemed to have a huge blind spot with those she loved. Why else had it taken her so long to realize Clark was Superman?

"So what am I missing then?" She asked. Caelyn looked her father to see if he would answer. He just bowed his head.

"I am not the only one who shares Dad's DNA. A secret agency stole his DNA and cloned him. I have spent the last month on the team getting to know my brother." All that pressure finally released, she let a few tears fall.

"Clark?"

"It's true, "he said sadly. He was so ashamed of himself. He knew avoiding this was pointless and this moment he realize just how stupid it was.

He turned to Caelyn. "Come here," he said opening his arms. She ran into them fiercely.

"I am so sorry I put you in that position. I was being immature and avoiding everything, including you and that was not right. I am sorry," he said stoking her hair.

"Good, Connor needs your help." Clark looked at her a bit confused.

"He needed a name. I named him Conner. It's a C name like us," she said looking up at him.

He keeled down to her level. "That shouldn't have been your responsibility, but I'm glad you did it," he said smiling.

"Weren't you going to go to Mount Justice for the weekend?" She nodded wiping the last of her tears away. "Good, why don't you leave a little early? Your mother and I need to talk," Clark said looking over at Lois, unable to read her expression.

They sat on the couch lost in their own thoughts. They had sat like that for over an hour.

"I just don't understand why you didn't tell me," she said looking at him. He had explained the stolen DNA and fears of what he may be capable, but Lois couldn't wrap her mind around why he wouldn't tell her. They were supposed to be partners. She could have helped. She wouldn't lie; it made her angry and made her wonder if their relationship wasn't what she had always thought was.

"I reacted badly from the start and even as I knew I was acting immature and stupid I couldn't stop myself. Even now I don't know why I let it get to this, why I fought it so hard. I guess that's why I didn't tell you. I knew when I told you that I'd have to admit to myself that I had made a mistake. I want to make this right now. I love you Lois, please forgive me for the enormous mistake I have made," he said grabbing her hands. Before Lois could answer, Clark heard a Crackle and Batman's voice enter his ear from his Comm.

Clark stood up quickly, all he heard was Red Tornado, Mount Justice and attack.

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	4. Chapter 4

Author's note- Thanks so much for the review, keep them coming!

Chapter 4

Clark had quickly explained to Lois something bad had happened at the Mountain before he flew off.

As he flew at top speed he realized he wasn't just worried for his daughter, he was worried about him too. Before this he thought he only worried about how he got here or what he might be capable of, but now he realized he cared about the boy.

He rushed through the zeta tube and soon found the aftermath of what ever occurred. The members of Young Justice were being assisted by their mentor. He quickly went to Caelyn and Connor, both incased in concrete next to Kid Flash. He quickly yet carefully used his heat vision to free the teens. Once they were free he grabbed his dust covered daughter. He had the urge to hug Connor, but he wasn't sure how he would take it so instead he opted for a shoulder grab. Neither teen missed it; Caelyn smiled and Connor looked a little confused.

"Are you both okay?" They both nodded.

Clark looked around. All the Young Justice members were okay and being attended to.

He took a big breath and looked to Connor. "Can we talk?" Connor looked to Caelyn and she nodded.

They made their way out onto the beach in awkward silence.

"I don't know how to start," Clark said sheepishly.

"You could just talk," Connor said earnestly, taking the statement a bit too literal.

"I guess I could." He stopped walking to look at Connor. He looked him over. He stopped at his eyes. He saw the nervousness and vulnerability. How could he have ever thought this boy a threat? What a fool he had been. He could tell Connor was uncomfortable as he broke eye contact and stared at the ground. Clark kicked himself. He had really messed this up, but at least now he could try to fix it.

"Listen Connor, I've been an ass." The statement was frank and it took the teen a bit off guard.

"I shouldn't have treated you the way I did. You did nothing to deserve it. You needed my help and guidance and all I could do was push you away. There is no way to rationalize what I did and the harder I try the more stupid it seems. I am sorry. You have every right to be mad at me and I won't blame you if you have no interest in what I'm about to offer, but please think about it." All this time Connor stood with unreadable expression, he may have been angry, but he continued to listen.

"I can't change what I've done, but that's over. I would like to make a change now. A new start if you will," he said anxiously awaiting his answer.

It was Connor's turn to study Clark's eye. The other times he had looked in his eyes they were full of shock and later anger. Now they were kind and pleading for a chance.

"So how do we start fresh?"

"One step at a time. How about dinner?"

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	5. Chapter 5

Chapter 5

Connor still didn't understand this world. He guessed it was just how life went, things constantly changing. Two week s ago he lived at Mount Justice and feared he would never really have a family, and now he had agreed to move into the Kent home and felt hope for a "real" family. Clark, Caelyn and Connor did all the moving; lifting heavy boxes with ease, while Lois on the couch with a smile on her face.

"You know, people say moving is a pain, but I just don't see it." The other three just looked at her and rolled their eyes as they headed up the stairs.

Connor sat on his bed as he, just taking it in when he heard a knock. He looked to the door to see Caelyn, his little sister, the one that he owed this all to. He smiled and waved her in.

"Didn't want to just barge into your room," she said. His room, he liked the sound of that. Sure he had a room at Mount Justice, but all the members did, this was something that was his. In his time here he wasn't sure if he had anything like that.

"Do you like it?" she asked breaking his train of thought.

"Yeah it's great," he said quickly.

"Good, just checking," she said. She hugged him and left.

He got up and unpacked a few of his things. He turned and saw Lois standing in the doorway.

"Hi." He liked her. She was kind to him. He especially liked how he noticed that she this unexplainable power over Clark. All she had to do was give him a look. It funny to him how the Man of Steel instantly reacted to his wife.

"I brought you an extra blanket and a lamp."

"Thank you."

"I hope this is comfortable for you."

"It is different from what I'm used to, but yes I like it."

"I'm glad. This is where you belong, I hope you know that."

"I'm starting to understand," he said with a small smile.

Lois left and Connor leaned back and laid on his bed, sleep quickly came to the boy.

Connor woke up. It was now dark, he looked to the alarm clock he had set up earlier and it revealed it was 3:18 a.m. He rolled over and laid there for a moment. He couldn't fall back to sleep so he pushed the blanket off of him that he didn't remember covering himself up with. As he swung is around to the side of the bed he looked at his feet, he also didn't remember removing his shoes. He thought it was weird, but he shrugged it off and mad his way to the kitchen for some water.

He got to the threshold of the kitchen and stopped, surprised to see Clark sitting at the table. Clark was absentmindedly playing with the rim of his glass when he looked up to see Connor.

"Hi."

"Hi."

I… um …. couldn't sleep," Connor stumbled.

"Neither could I."

"I was just gonna get some water."

"Cups are in the cupboard to the far left." Connor moved and filled the glass from the tap. He hovered by the sink nervously sipping his water.

Clark could feel the tension, the awkwardness Connor felt, he had caused it and now he needed to do all he could to fix it.

"Connor, come sit here for a minute." The boy came slowly and sat across from him.

"My parents found me in a spaceship in a field. They had no idea where I came from or what I was capable of, but they took me in and loved me. We are so similar that there is no way for me to deny that you are part of me. I am sorry I ever tried. I just want you to know that, and one day I hope we can truly put it behind us." Connor was a little taken by his pure honesty and the pain in his face. He opened his mouth to respond when he could tell Clark had picked up something with his super hearing.

"What is it?"

"Apartment fire downtown."

"Let's go."

"Cononr…"

"Please."

"Okay, but stay close."

"That's not exactly my style."

Clark had quickly changed into his suit and when he stopped spinning Connor was now faced with Superman. He gave Connor a look, one not as intimidating as the Bat-glare, but one conveyed he meant business.

"Okay, your town, your rules, got it."

By the time they got to the scene the building was engulfed in flames. Superman went up to the fire chief for details with Connor close behind.

"Superman, glad you are here. My men are fighting from the outside, but the fires burning to hot and the building is too unstable.

"Is anyone inside?"

"There were reports of a little girl."

Superman huffed out a breathe, ready to take on the fire, but before for he could he saw a streak of black and red move from his side and into the building.

"Superboy, wait."

Suddenly, Clark heard a series of noises and just a moment later the building exploded.

Superman froze as the smoke billowed up. He snapped himself out of the shock that was setting in and ran fast and hard towards the rubble that was once a building. He had no idea where he was, he just began to dig. He kept his ears trained for the smallest sound. It seemed like he had been digging for hours before he heard a small cough. He ran towards it and moved the heavy rubble aside. He saw him, his clothes torn and burned, barely hanging onto his frame. He gently rolled him over. To his surprise he saw a young girl under him. She was coughing and shaking, but otherwise unharmed. He yelled to the firemen who removed her. He then turned his attention to the unconscious boy before him. He assessed his injuries. He had a large cut on his head and burns on his arms. He scooped up the boy and hoped that his injuries were nothing a day in the sun couldn't heal.

He laid him down on the couch quietly, as not to wake Caelyn or Lois. God, Lois would kill him when she found out. He went up to Connor's room and rummaged through a box labeled "clothes" to find something to change the boy into. He then gathered a large bowl of water and first aid supplies. Clark worked quickly washing the dirt and debris from Connor, changing him into fresh clothes then cleaning and dressing his wounds. It wasn't until he was tending to his head wound that the boy stirred.

"Ow."

"It's okay, don't move, "Clark soothed.

"What happened?"

"Explosion," Clark said a little curtly.

"Sorry."

"I told you to stay with me."

"I'm sorry."

"You scared me. I thought that maybe…." Clark trailed off.

"Listen I'm really sorry."

"You acted impulsively, but I'm glad you did. You saved that little girl." Connor smiled broadly.

"But next time, try not to get yourself blown up. You invulnerability still has limits," Clark said pointing to his bandaged arms.

"Now let's get you to bed." They made their way up the stairs.

Connor laid down in his bed and reached for the blanket, but not before Clark grabbed it and covered him. Connor now realized how he had been covered up earlier.

"Goodnight Connor." He squeezed the boys shoulder. He made it to the door before turning around.

"I'm proud of you," he said before shutting off the light and closing the door.

Connor pulled the blanket up closer around him and fell asleep with a smile on his face.


	6. Chapter 6

AN- Sorry I meant to post sooner, but life got in the way. Anyway here is the next chapter, enjoy-Eri

Chapter 6

The mission had been a success. They were able to plant hidden camera feeds in the warehouse that the Justice League believed was a new place of production for venom. What the team didn't know was they were the only ones watching the warehouse.

Lex Luthor entered his office, Mercy waiting for him.

"Anything interesting on the feed?" I want to know what to expect if I complete this deal."

"Not what you were expecting, but I trust you will find it interesting." Luthor watched with interest as a group of teens dropped down from the ceiling and proceeded to set up hidden cameras.

"Freeze it, zoom in. Look there; there is Superboy and look at that. I guess Superman found his own way to reproduce his DNA," he said pointing to the frozen image of two teens standing side by side both sporting the "S" shield.

"Well this certainly changes things."

Jonathan Kent pushed his empty plate away, very full and content. It is was a beautiful evening to be sitting outside and eating a great meal with his family, especially with his newly discovered grandson. As everyone finished eating Caelyn and Connor cleared the dishes.

Martha Kent looked back in the direction they had gone. "So how is he adjusting?"

"Good, he's great. I just can't help but still feel guilty for the way I treated him. If Caelyn hadn't..."

"Blackmailed you?" Lois piped in with a slight chuckle.

"Don't beat yourself." Jonathan comforted.

"I know, but I can't but think of how you guys found me and took me, I should have…"

"Clark there were different circumstances and you are making it right now. No sense dwelling on things you can't change, just focus on what you can."

Just then Caelyn and Connor came back out. Caelyn had a football in hand.

"Connor got a kick out of your old football picture, Mr. Star Quarterback. We found this in the closest. Wanted to see if you could still throw it? "Caelyn said with a sly smile.

"Are you teasing me Caelyn Lane?"

"I wouldn't dare," She said in mock shock. "but it would be fun to play."

"Well…"

"Aww, come on Dad," Connor said. His eyes locked with Clark's. It was the first time, and the guilt Clark was feeling washed away. It was true he couldn't change the past but he was going to enjoy the present and the future.

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	7. Chapter 7

Chapter 7

The team was sparing 2 vs. 2. It was Aqualad and Artemis vs. Robin and Supergirl. Superman had come to watch that afternoon's training session; he stood next to batman who was also observing. As the sparing began Clark couldn't help notice how Aqualad and Artemis were sharing verbal queues as to the next move while Robin and Supergirl would just look at each other. He found it uncanny how the two knew each other so well. He made him think back to when he had taken his daughter to Gotham to meet Bruce's new ward.

"_Hi Uncle Bruce," Caelyn said with a smile._

"_Hello Caelyn. Dick should be in the living room, go on in." After Caelyn passed the two superheroes Bruce gave Clark a Batglare. _

"_She knows she is the only one that gets to call me that." _

"_She knows" _

"_You encourage her don't you Boy Scout?" _

"_Maybe," Clark gave a smirk. _

_Caelyn walked into the living room on the manor. The TV was on but no one was watching it. She looked around for the boy she was supposed to meeting today, but didn't see him anywhere. Suddenly she heard a voice coming from above her. She looked up to see a boy with black hair and intensely blue eyes hanging upside down from the rafters and waving at her._

"_Hi, I'm Dick." _

"_Hi, I'm Caelyn." She turned her head sideways and raised an eyebrow. "What are you doing up there?"_

"_Oh just hanging around." Both nine year olds were laughing up a storm when the adults entered the room._

Bruce watched with interest as he saw his son and Clark's daughter share a look. They both nodded slightly and suddenly Caelyn did a foot sweep on Artemis while Dick flipped over her and did a swift kick to Aqualad's chest. Both of the older teens went down and the sparing match was over.

Clark was interested to see the next sparring match, but his super hearing altered him to a situation that needed his attention. He made quick nod to his kids before heading for the zeta tube.

Connor and Caelyn were leaving Mt Justice after the intense training session. All both of them wanted to do was go home and get some dinner.

"I was surprised that you and Wally were able to work so well together in the sparring match."

"Well we can't all have a weird almost physic connection with our partner," Connor said as he stepped into the zeta tube.

"No, just with your girlfriend," She called after him. Caelyn looked back a Dick who was talking with Bruce about something. He must have felt her eyes on him because he turned and waved quickly before turning back to Bruce.

Caelyn exited the zeta tube and was met with white hot pain. She fell to her knees instantly, struggling to breath against the pain. Before her world went dark she saw Connor standing eerily still staring emotionlessly forward.

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	8. Chapter 8

Author's note- Thanks for the reviews, I really appreciate the feedback. Now for the next chapter!

Chapter 8

Caelyn was awake but the pain was surrounding her. She was afraid to move, but slowly she opened her eyes. She gasped at her surrounding, but quickly regretted her reaction as the gasp turned into a painful coughing fit. The reason Caelyn felt the pain surrounding her was because it literally was. She was in a cage with Kryptonite bars. She forced her eye to open again. She looked past her prison to what was outside the cage. She saw Connor he was still standing still with the same vacant look on his face. She did not understand what was going.

"Con...," she tried to whisper weakly but was cut off with coughs. He did not respond, but someone else did.

"Good to see you are awake. Supergirl, I presume?" She had never met him but she was well aware who was standing in front of her.

"Luthor."

"What did …..you do to him?"

"Oh, nothing much just gave him a couple words of wisdom. It is amazing what two simple words can do."

"What are you talking about?"

"The Justice League is so trusting. They should do a little research before taking in strays. You all welcomed Superboy in, but no one really asked how he was created." Caelyn was trying to focus on Luthor's words, but it was hard, her head was throbbing and her senses were fuzzy. The only thing that was clear was the pain.

"You see Superboy here," Luthor gestured to the still boy, "is only half Kryptonian. To make the clone controllable we needed to add human DNA. You can say it was it was my pet project so a graciously offered my contribution."

"No." Caelyn couldn't conceive of this. She was having trouble keeping her eyes open , but despite all the pain she couldn't believe it . She had been raised to fear this man and her he was he had created her brother with his evil DNA.

"Oh yes young lady. He is part of me and I have control over him that he wasn't even aware of." Luthor went over to Connor and snapped his fingers in his face. With that one action Connor was back and he was suddenly susceptible to the pain Caelyn had been enduring. He fell down fast. Luthor bent down and whispered something in his ear. Connor eyes were again strictly focused, but they were trained on Luthor. Connor got up slowly

"Good boy. You don't want to be in pain again and I can keep you from harm. I just need to kill her.

Luthor unlocked the door of the cage and Connor entered the cage. Somehow the Kryptonite was not affecting him. Caelyn used what was left of her strength to move to the furthest corner of the cage. It was all she could do. Her body was shaking as her brother approached. She took a ragged breath.

"Please, don't do this. Fight his control. I love you, please Connor." She watched as he stopped in front of her. Somehow it seemed that saying his name had gotten to him.

"Caelyn," he whispered. As he came out of the trance the pain invaded and he fell to the ground next to her.

"Well, the project failed, but at least you will both be dead," Luthor said matter-of-factly as he locked the door and left. The teens lay next to each other shaking in pain.

Clark got home later than expected. He came to find Lois sitting on the coach reading. She turned when she heard him descending the stairs.

"Are we warming up dinner or did you and the kids already eat?"

"The kids aren't here?"

"They must still be at the cave."

"Yeah, but I told to come home for dinner before I left."

"Maybe they just lost track of time."

"Yeah, maybe. I'll just check."

"Superman to Superboy"

All he got was static.

"Connor do you read me?"

Nothing.

"Supergirl please respond"

He was greeted by static.

He looked to Lois with concern.

"Maybe they are still at Mount Justice?"

"Superman to the Mountain Justice."

"Yes, Superman?" Red Tornado replied.

Are Superboy and Supergirl still there?"

"No, they left some time ago."

Lois watched as Clark's face changed and she knew something was wrong.

"How long ago?"

"Over three hours."

Lois saw Clark's face pale and his eye get big.

"Superman to Batman."

"What is it Clark."

"My kids are missing. Meet me at Mount Justice."

"On my way."

Superman got to Mount Justice and was trying to figure out what was going on. Batman soon joined him accompanied by a visibly anxious Robin. The rest of the team had still been there.

"I don't get it how do they just disappear, I mean they are super." Artemis said.

"It's got to be something major," Wally chimed in.

"Will you shut up KF?" Robin snapped.

"Sorry"

"That's enough," Batman said. "The zeta tubes report they left at 4:47 p.m. together."

"So we retrace their steps," Kaldur said.

"It's the best place to start," Superman trying to remain level headed.

"Alright but let's split up.

"Superman, Kaldur, Robin and I will go through the zeta tube to Metropolis," Batman said. "The rest of you will follow in the bio ship. Red Tornado and Black Canary will remain behind here."

They broke up determined to find the two missing team members.

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	9. Chapter 9

Author's note- Alright, thanks for the reviews. I have one more chapter for this story then I am working on a sequel. Thanks and review!

Chapter 9

Superman, Kaldur , Robin and Batman were in the ally where the zeta tube let out. Batman bent down and picked up the two destroyed comms.

"They were taken here. It had to be a strong planned attack," Batman said.

"Kryptonite." Superman bowed his head almost feeling the pain.

"It is the most logical deduction. What else could have subdued them?" Kaldur asked.

"So now the questions now are who and where?" Batman replied.

"Tire tracks, big ones, most likely a van, " Robin said from the edge of the ally were he had wandered. The other three made their way over and Robin was already furiously typing on this wrist computer.

"Robin?" Kaldur asked.

"We know when they were kidnapped. The car went right…" Robin pointed to the tire tracks, but was cut off by Batman.

"Using the speed cameras and ATM cameras in the area, we can track the vehicle. "

Robin watched intently. A dark blue van exited the ally onto the main road at 4:52 p.m. The four watched the van made turn after turn and the images jumped from one camera image to another.

"Freeze." Superman nearly yelled suddenly. "Zoom in." Robin did as he was told and the driver's image was revealed. Even though it was disgusted with a mustache and wig, it was still clear to the heroes.

"Luthor." Superman spat with venom.

A minute or so more passed and Robin had the location pinpointed as close as possible from the last camera that captured it.

"The van went into the warehouse district."

"Let's go."

After searching a few warehouses they had finally found the right one. Miss Martian had concentrated and detected Connor's weak thoughts.

Alright, Miss Martian get the bio ship ready. Artemis guards the door. The rest of you come with me. Superman started to follow those going into the building.

"Superman, you should stay here.

"Batman, I have to go in there."

Batman then lowered his voice. "Clark you know you can't. We know there is Kryptonite."

"I have to. These are my kids Bruce." Superman whispered the last part.

"That is why I'm being objective." He glanced over to Robin. "If it were me I'd expect you to do the same. "

With that Batman, Aqualad, Robin and Kid Flash headed into the dark warehouse. They headed to the back and it wasn't long before the saw the eerie glow from the cage. They could see the two superkids laying still next to each other –to still. Their bodies were contorted in pain, but neither was reacting to it.

"My God." Batman muttered under his breath. He moved quickly to pick the lock on the cage. Aqualad and Kid Flash went in and got Superboy of the cage. Robin didn't wait for Batman, he grabbed up Caelyn and made his way out. Once they were outside of the warehouse Robin stopped.

"Robin?"

"She's not breathing." Robin began to preform CPR.

Everyone outside the ship froze. The minutes added up and Batman moved to put a hand on his son's shoulder.

"Robin…"

"Just another set and …." He said breathlessly as he did compressions.

Clark stood still, not daring to move. He couldn't go in, so he waited. He had watched closely as the team brought his son past him and onto the ship. He had felt hope then, hope that it would be alright. All he needed was for Caelyn to come out and it would be okay. He had seen Robin carrying her toward him and he breathed a sigh of relief, but then he stopped.

Batman turned to Aqualad, Kid Flash and Airtimes who stood silently nearby.

"Get on the bio ship, get Superboy back to the cave. He needs medical attention."

They solemnly nodded. Airtimes grabbed Wally's hand as they went aboard.

"We can't leave her!" Clark said as he finally moved and started toward his daughter. Batman moved fast and caught him by the shoulders. He talked to him quietly.

"Clark, Clark. You need to focus on Connor. He needs help now."

"But…I …can't. I can't leave her. I need to take care of her." The man of steel's tears streamed down his face.

"I will take care of her. We will bring her soon. Go take care of Connor. "Clark numbly nodded. Batman looked to Aqualad who still stood outside the ship.

"Aqualad, get him on the ship, come back for us once you've gotten the others back." Aqualad nodded as led Clark onto the ship.

The team arrived back to at the cave. Kid Flash and Miss Martian raced Superboy into the medical ward where other League members waited to treat them. Flash and Martian Manhunter turned to Superboy aware they would be treating only him.

Lois had been waiting with Wonder Woman who had come to get her when the League had been made aware of the magnitude of the situation. Lois was not a patient person and the waiting was killing her. When the teens had brought Connor past her, she breathed a sign relief. Her eyes strained in the direction they had come from to see her husband and their daughter, so she could be okay- so her family would be okay. When she saw Clark coming towards her, Aqualad slightly guiding him, her knees went weak. She managed to run to Clark, grabbing him by the shoulders.

"No! No, where is she? Where is my little girl?"

"Lois…she… I'm sorry." With that they both collapsed in each other's arm, grasping at what comfort they could find.

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	10. Chapter 10

Author's note- So here it is- the last chapter. Please review and let me know your interest in a sequel.

Chapter 10

Dick wasn't sure when he had finally stopped CPR. It may have been when Bruce screamed and removed his cowl after punching a brick wall. He watched him now. He paced, cursing under his breath .He had turned towards them and looked down at Caelyn, and her pale unmoving form brought a tear to his eye. He turned away quickly. Dick didn't want to look at her, but he still held her hand. He didn't want to let go. With his free hand he rubbed his masked eyes, allowing a trapped teardrop to escape. It fell down and landed on Caelyn's cool wrist. Dick touched it tenderly. He wiped it away, but let his fingers linger there. That's when he felt it- the light uneven palpitation of her pulse.

"Bruce!" Dick screamed.

By the time Bruce turned he saw Dick preforming CPR again.

"She has a pulse."

Kaldur had really come to care for his teammates. This situation and the pair in front of him sincerely broke his heart. They shouldn't have to grieve for the loss of a child. Caelyn had been so full of life, she was simply too young to be gone. He bowed his head in reverence when the crackle presented in his ear.

"Aqualad, get here now."

Together at his bedside, Lois and Clark stared at Connor. He was still unconscious, but with the sun lamps shinning down on him, they were told he should be fine. The both stared at him willing him to wake up, so they would know. So they would know that they still had a child. They were both trying hard not to think of it, to focus on Connor. It was hard though, every time their eyes met they thought of her, so they looked at Connor.

Suddenly their vigil was interrupted by a commotion outside. They looked at each other as the doors to the medical ward open and Batman brought Caelyn in and laid her down on the bed next to Connor. Martian Manhunter prepped a breathing tube and Black Canary set up more sun lamps.

"What… "Clark stammered.

"I told you we would bring her back." Batman said with a small smile as he put a comforting hand on his shoulder. "Although, I'm not the one to thank." He nodded to Robin.

Lois moved from her daughter's side and pulled Robin into a hug. "Thank you."

All the League and team could do was wait and it seemed to everyone that was all they had done. For over a day they waited anxiously for the superkids to wake.

Caelyn was very confused. She was extremely sore and she was having problems breathing. She felt like something was stuck in her throat. She tried to cough, but that only made it worse. She knew there may be some explanation if she opened her eyes, but she was afraid to be greeted by that horrible green glow or worse. Suddenly she started to hear things, muffled voices. They were comforting her and suddenly it was easier to breathe. They were now coaxing her to open her eyes, but she didn't want to. She was too afraid of what she might see.

"Cae, please open your eyes. You are safe. It is okay now." Her father's voice was suddenly clear. She felt both her hands being held and she felt safe. She slowly cracked open her eyes.

Caelyn opened her mouth but nothing came out but a raspy squeak. Lois handed her a cup of water and she gratefully drank it. She looked to her parents.

"Hi."

"Really after all this, and the first thing is a casual salutation." Clark laughed dryly. "You have no idea how close … God, come here," Clark said grabbing his daughter up into a hug.

She was hugging Lois when she seemed to realize something and pulled away.

"How is Conner?"

"He is still sleeping, but he should be fine," Clark said nodding towards his bed.

"There is something you should know about him, about how he was created."

"Shhh, we can talk later, just rest," Lois said stroking her hair. Caelyn could see the fear in their eyes when they looked at her. It made her understand the gravity of the situation.

"That bad, huh?"

"Yeah," Clark answered simply.

"We almost lost you, well actually we did lose you for a bit, but he brought you back." Lois nodded off to the side where an exhausted Robin slept. He was curled into a chair, his domino mask slightly crooked on his face.

As if feeling eyes on him, Robin opened his eyes. He shook his head, not sure if what he saw was real. Caelyn was sitting up in bed and staring at him.

Before he could move she spoke. "You saved my life?"

"Well yeah, if not I would be the youngest on the team again," he said moving to her and giving her a hug.

"You are only four months older than me Dick, but thanks."

"I don't like these." Caelyn said after a minute, pointing to the sun lamps

"But they are helping you heal." Lois said

"It feels fake. Can I go outside?"

"I don't know sweetie," Clark started.

"Please? I want to feel the sun on my face. I know it will make me feel better."

"Alright, but Robin go with her."

"Yes Sir."

Caelyn started to get up. Her legs were wobbly when she first stood, but her parents steadied her.

She moved over to the other bed and leaned down to Connor. She kissed his head and whispered to him.

"You need to wake up. It doesn't matter, none of it. You are my brother and I love you. I will tell them now, but they will still love you too. " She turned to her parents. "When we were kidnapped, Luthor said things. He said that Connor is not fully Kryptonian. He is only half like me, but he told me who the human DNA came from. "She paused.

"Who?" Clark asked anxious.

"Luthor."

"Oh God, that monster how dare he." Lois said hugging Clark. The both looked over to him.

"I think that might be why he hasn't woken up yet. I think he's afraid we won't love him."

"Of course we do." Clark said. "Why don't you go outside now, but take it easy.

"Okay," Caelyn said as she made her way to the door, Robin following close behind. She shivered ever so slightly; he grabbed the blanket from the bed and draped it over her shoulders.

They made their way out of the cave after passing by members of the league and team happy to see her awake. Caelyn hugged M'gann as they passed whispering that Connor would wake up soon. When they got outside they headed for the beach. They walked along the ocean for a few minutes before Dick realized she was leaning on him heavily and they sat down. The watched the waves in silence. They didn't say anything; they didn't need to. Dick grabbed Caelyn's hand and laced their fingers. They looked at each other and smiled.

Clark sat with Connor; Lois had left to get something to eat. He stared down at his son- that was what he was, this would not change that. He grabbed his hand.

"Connor, I don't know if you can hear me, but it's time to wake up. I know you might be scared, but let me tell you something. You are my son. Nothing can change that. You have my name and my love. I need you to wake up so our family can be whole again. I love you Connor. "A minute passed before Clark felt his hand being squeezed. Clark looked to his face and saw his eyes slowly open.

"Connor." He breathed in relief.

"Dad."

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